This is the default functionality of odoo. I observed that in the sales order if there is a service type product (not deliverable product) then this product will not be listed out in the delivery order but in the procurement expecption it will listed out with confirmation status.
When we confirmed the delivery order the system will deliver the non service type product and their respective procurement status move to done stage but service type product still remain in the confirmed stage.
That is why in the sales order "delivered" not being checked off. and sale order not goes to Done state, so after service period completion we need to manually change state of that procurement to done, automatically sale order goes to done state.

Out of curiosity, what action do you have assigned to complete the SO? I would suspect that the intial version8 has a default testing action and was removed, or that another cross-configuration setting may govern this.

In the realm of one type of JIT manufacturing configuration;

• Order is confirmed by Purchase Order.
• SO is generated -> Sends Production order and Procurements -> Produced -> Stock is placed in inventory -> SO closed.
• Invoice is created -> Sends Packing Slip to Shipping -> Order is Shipped -> Invoice is sent to customer.

I have found out what could be the problem

#1 - I have a number of products set to MTO

#2 - These products do not have supplier assigned to it

#3 - When the Sales is generated with MTO products, the PO gets drafted. For some reasons these POs are tied to the SO and determines if the products are delivered or not,

#4 - Office staff manually created the PO for and completed the PO. Sales are then completed, stock delivered, but in Sales Order the delivered checked box is not checked.

#5 - When I click on the item in the order line, ERP shows that the order is not done, but still on order. These orders are actually already delivered.

#6 - If I go to Warehouse, Stock Move, these items are still WAITING AVAILABILITY. Manually setting them to done does not change the status to delivered.

#7 - When I go to warehouse -> procurement exception, I still see these items sitting here with the exception of no supplier define. If I cancel and delete these autmatically generated PO the deliver order gets deleted as well and I need to regenerate the deliery order. Now if I regenerate delivery order and deliver these orders out, the delivery box will still be left unchecked. 

I need to examine #6 onwards.

In Summary, to create the problem:

#1 - Create a Product and set it to MTO

#2 - Go to sales order and generate a sales for this product.

#3 - receive payment for this product so the Sales invoice part is completed.

#4 - Manually create a PO for this product, receive the order into warehouse, and the pay off the supplier so PO is completed.

#5 - Go to warehouse and deliver off this product so that Sales Order should be set to done.

#6 - Go to sales order and verify that the order is still not set to done but is in sales order state.

#7 - Click on the order line to see that the order is not set to DONE even though the order has in fact been delivered.

#8 - Go to warehouse and then deliver products, find the product and set it to done.

#9 - Go back to #6, #7, you'd find that Sales Order is still not done.

#10 - Go to Warehouse -> Procurement Exception and you will see the exceptions there. Try to cancel and delete them off then go back to the Sales order.

I haven't fixed the problem, I'd like to be able to fix this properly than creating an action to force this as done.